Mackey was born on August 15, 1953 in Houston, Texas, to Bill and Margaret Mackey. He has a sister and a brother.

Bill Mackey was a professor of accounting, CEO of LifeMark, a health-care company, and investor of Whole Foods Market, before he died in 2004. In the abstract to the book: Conscious Capitalism, Mackey thanks his father for teaching him valuable life lessons.[3]

Mackey’s mother, on the other hand, did not influence him in the same way. Margaret Mackey died in 1987, making John thirty-four years of age when he lost his mother. John and Margaret had a strained relationship, partly due to her desire for a different future regarding her son. Margaret felt that such a “fine mind” should devote their time doing something more productive than retailing. John did not agree, but in later years he regretted that he did not make it more clear that he loved her.[4]

Mackey co-founded his first health food store, SaferWay, with his girlfriend Renee Lawson (Hardy) in Austin in 1978. They met while living in a vegetarian housing co-op.[5] They dropped out of college.

They borrowed $10,000 and raised $35,000 more to start SaferWay. At the time, Austin had several small health food stores. The two ran the market on the first floor, a health food restaurant on the second, and, for a short time, lived in the third story of their building. In two years, they merged SaferWay with Clarksville Natural Grocery run by Mark Skiles and Craig Weller and renamed the business Whole Foods Market. All four (Mackey, Hardy-Lawson, Skiles and Weller) are considered co-founders of the business.[5]

Mackey built Whole Foods into an international organization, with outlets in major markets across the country, as well as Canada and the United Kingdom. Along the way he bought out smaller competitors. In 2007 Whole Foods purchased a major natural foods supermarket competitor, Wild Oats Markets, Inc.

Whole Foods was the first grocery chain to set standards for humane animal treatment.[2] Mackey was influenced by animal rights activist, Lauren Ornelas, who criticized Whole Foods' animal standards regarding ducks at a shareholder meeting in 2003. Mackey gave Ornelas his email address and they corresponded on the issue. He studied issues related to factory farming and decided to switch to a primarily vegan diet that included only eggs from his own chickens. Since 2006, he has followed an entirely plant-based diet. He advocates tougher animal standards.[8]

Despite Whole Foods' welfare standards, Mackey has been criticized by abolitionist vegans such as Gary L. Francione, who believes the Whole Foods company policies betray the animal rights position.[9] By other[who?] accounts, Mackey is the "driving force"[attribution needed] behind significant changes in animal welfare. For instance, he started a non-profit foundation, the Animal Compassion Foundation, to address making animal welfare more economically viable.[10] The Animal Compassion Foundation folded in 2008 with the formation of the Global Animal Partnership, a nonprofit organization that is independent of Whole Foods Market. Mackey is on the Board of Directors of Global Animal Partnership.[11] Additionally, he is a board member of Farm Forward, a 501(c)(3) nonprofit organization that implements innovative strategies to promote conscientious food choices, reduce farmed animal suffering, and advance sustainable agriculture,[12] and he has been a member of the Board of Directors for the Humane Society of the United States since 2009.[13]

In 2006, Mackey announced he was reducing his salary to $1 a year, would donate his stock portfolio to charity, and set up a $100,000 emergency fund for staff facing personal problems.[14] He wrote: "I am now 53 years old and I have reached a place in my life where I no longer want to work for money, but simply for the joy of the work itself and to better answer the call to service that I feel so clearly in my own heart."[15]

Mackey co-founded the organization Freedom Lights Our World (FLOW) to combine his commitments to "economic and political freedom as well as personal growth, social responsibility, and environmental stewardship."[20] He supports such changes as green tax shifts, environmental trusts, world legal systems to allow the poor to create legal businesses, and a citizen's dividend to help the poor in the developed world.[21] The name and focus of FLOW have since become Conscious Capitalism, Inc., which was initially created as a program of FLOW and evolved to the point at which it became the organization's principal focus. In 2010 the name of the organization was formally changed. The Conscious Capitalism Institute was chartered in 2009. In 2010 the original FLOW group merged with the Institute group to become one unified organization.[22] In 2013 Mackey was interviewed on Harvard Business Review's Ideacast podcast about his views on Conscious Capitalism.[23] Mackey said, "If you want to be competitive in the long term, your business needs to have discovered its higher purpose and it needs to adopt a stakeholder philosophy." He eschewed the conventional thinking that "business has to be sort of ruthless and heartless to be successful".[24]

In August 2009, Mackey wrote the editorial in the Wall Street Journal expressing his viewpoints on universal healthcare in the United States.[28] "While we clearly need health-care reform, the last thing our country needs is a massive new health-care entitlement that will create hundreds of billions of dollars of new unfunded deficits and move us much closer to a government takeover of our health-care system," he wrote. He continued: "Many promoters of health-care reform believe that people have an intrinsic ethical right to health care—to equal access to doctors, medicines and hospitals. While all of us empathize with those who are sick, how can we say that all people have more of an intrinsic right to health care than they have to food or shelter?"

In an NPR interview in 2013, Mackey compared the Obama administration's healthcare law to 'fascism' instead of socialism, stating, "[t]echnically speaking, it’s more like fascism. Socialism is where the government owns the means of production. In fascism, the government doesn’t own the means of production, but they do control it — and that’s what’s happening with our health care programs and these reforms."[29][30] The day following the interview, Mackey wrote in a blog post that he regretted having made the remark, stating that he "made a poor word choice to describe [the U.S.] healthcare system."[30][31] Instead, he called it 'government-controlled health care'.[30]

Mackey is known for his strong anti-union views, having once compared unions to herpes in that "it won't kill you, but it's very unpleasant and will make a lot of people not want to be your lover."[7] Whole Foods Market, along with Costco and Starbucks, teamed up in 2008 to create an alternative to the Employee Free Choice Act. The three companies invited other corporations, unions and public interest groups to join them, proposing instead that unions be given more access to meet with workers, stricter penalties for labor violations and a guaranteed right to request secret ballots in all circumstances.[32]

Mackey commented in 2005:

"It's illegal in the United States for there to be company unions — special unions which are formed and controlled by the employees and managers of the company to represent their interests and collectively bargain on their behalf. These type of unions are legal in many countries such as Japan, but are illegal in the United States. Instead the law requires that all unions be outside unions. I believe this law should be repealed and that company unions should be as legal as any other kind of voluntary association."[33]

In a 2010 discussion of books on his reading stack with journalist Nick Paumgarten, Mackey explained his views on human-caused climate change were similar to those of Australian geologist and author Ian Plimer:

...Mackey told me that he agrees with the book [ Heaven and Earth ]'s assertion that, as he put it, "no scientific consensus exists" regarding the causes of climate change; he added, with a candor you could call bold or reckless, that it would be a pity to allow "hysteria about global warming" to cause us "to raise taxes and increase regulation, and in turn lower our standard of living and lead to an increase in poverty."[4]

On July 20, 2007, The Wall Street Journal[35] revealed that Mackey was, for at least seven years, using the pseudonym "Rahodeb" (an anagram of his wife's name, Deborah) to post to Yahoo Finance forums. He referred to himself in the third person and criticized rival supermarket chain Wild Oats Markets.[36] The Federal Trade Commission[37] approved a complaint challenging Whole Foods Market’s approximately $670 million acquisition of its chief rival, Wild Oats Markets, Inc. It authorized the FTC staff to seek a temporary restraining order and preliminary injunction in federal district court to halt the deal, pending an administrative trial on the merits. After an extensive regulatory battle with the FTC, a federal appeals court consented to the deal. Whole Foods officially completed their buyout of Wild Oats on August 27, 2007.

In May 2008, after an SEC investigation cleared him, Mackey started blogging again. In a 2,037 word post, he wrote about why he began blogging in the first place and how his upbringing drove him to defend himself and Whole Foods. He admitted he made a mistake in judgment, but not in ethics.[38]

On December 24, 2009, Mackey resigned from the position of Chairman of the Board of Whole Foods Market, a position he held since 1978. On his blog he said, "John Elstrott will now take the title of Chairman of the Board, which will accurately reflect the authority and the responsibilities that he has had for many years." Mackey remains a member of the Board of Directors.[39]

Even though John Mackey's bank account consists of millions of dollars, and his company has a market value of $11.7 billion (2011), is he living a modest life, driving a fire-year-old Honda Civic, renting the cheapest hotels and always flying commercial. At business meetings is he wearing Khaki shorts, a checked shirt and some old running shoes.[40]

During his twenties, experimented he with different religions and philosophies. Because of a girl, became he Christian for a short while. Now he recognizes himself as a perennialist, also called the Perennial philosophy. Which is a person that believes a universal truth lays beneath everything.[41]

He married his current wife, Deborah Morin, in 1991.[42] They have no children. Both practice yoga. They spend the week in Austin and weekends at their 720-acre (291.4 ha) ranch 40 miles (64 km) west of Austin.[5]

FLOW A non-profit co-founded by John Mackey that is dedicated to "liberating the entrepreneurial spirit for good" and described as "a transpartisan movement combing idealistic initiative with free enterprise principles to systematically work toward a better world."